Sam Harris comes out swinging. He's not going to win on finesse, but he has the brute force of reason and facts on his side.
Andrew Sullivan, interestingly enough, reproduces only Harris's rebuttals to Sullivan's own points. I don't think Sullivan has accurately reproduced the "flavor" of Harris's comments, but he does honestly reproduce a substantive rebuttal.
The actual truth of Sullivan's religious beliefs is, of course, indefensible. Nor has Sullivan (to compliment him) even begun to master the sort of philosophical doubletalk under which theistic philosophers--especially Christian theistic philosophers--bury their underlying irrationality.
It's still kind of irritating reading Harris's work, though. Harris is good at compling lists of religious stupidity, irrationality, hatefulness and violence. But he seems to have a hard time focusing on what I see is the fundamental point: That the (relatively) mild irrationality of moderate religion just feeds and supports the virulent, severe irrationality of fundamentalist religion.
Moderate religion relies on the exact same epistemic basis (scripture and tradition) as fundamentalism; on that basis, fundamentalism has a stronger case. The only bases a moderate could possibly distinguish himself from a fundamentalist are conscience and skepticism, which lead inexorably to epistemic relativism or nihilism.
 I.e. bullshit.
 In just the same way as the mild irrationality of moderate conservatism just feeds and supports the virulent irrationality of neo-conservatism, and sometimes as moderate leftism feeds fundamentalist leftism.
 I personally hold ethical epistemic nihilism and meta-ethical relativism: We can't know that any moral belief is true just because moral beliefs are not truth-apt. Lacking any epistemic basis, we have no choice but to rely on the relativistic meta-ethical techniques of propaganda and negotiation. Then again, I'm an liberal atheist, not a conservative moderate Catholic.